FHIR Chat · Contributing to HAPI - Getting Started · hapi

Stream: hapi

Topic: Contributing to HAPI - Getting Started

Kevin Mayfield (Mar 26 2019 at 06:19):

Is their a guide?

I've done the basic's at the moment. Downloaded source from git, mvn clean and in the process of mvn install.
(It's the HAPI FHIR Validation I'm looking at working on - for UK+stu3)

Is their any special config?

Kevin Mayfield (Mar 26 2019 at 06:57):

Java version (8?) maven (3.5?)

Grahame Grieve (Mar 26 2019 at 07:21):

you're better off to use the java code directly without HAPI

Kevin Mayfield (Mar 26 2019 at 07:23):

We do that at present but their are a number of bugs we want to fix

Kevin Mayfield (Mar 26 2019 at 07:23):

(and also diagnose operationOutcome error messages)

Grahame Grieve (Mar 26 2019 at 07:24):

are you running the R5 validator?

Grahame Grieve (Mar 26 2019 at 07:25):

if you mean, you're running the validator jar, and you want to fix bugs in it. then you want the hapi core code, and the fhir github code, and not the rest of FHIR

Grahame Grieve (Mar 26 2019 at 07:25):

or HAPI

Kevin Mayfield (Mar 26 2019 at 07:31):

Yep that's what I've looking at. At the moment we have a couple of classes to add in UK support in our 'argonaut' demonstrator' [https://data.developer.nhs.uk/ccri]

Grahame Grieve (Mar 26 2019 at 07:32):

hmm what do they do?

Kevin Mayfield (Mar 26 2019 at 07:34):

First bit we add UK profiles to the DefaultProfileValidationSupport

    ValidationSupportChain validationSupportChain = new ValidationSupportChain();

    validationSupportChain.addValidationSupport(new DefaultProfileValidationSupport());
    validationSupportChain.addValidationSupport(new CareConnectProfileValidationSupport

Grahame Grieve (Mar 26 2019 at 07:34):

so that bit has nothing to do with the validation.jar

Kevin Mayfield (Mar 26 2019 at 07:35):

Next issue: https://github.com/jamesagnew/hapi-fhir/issues/1235

Grahame Grieve (Mar 26 2019 at 07:36):

so the next thing: the only supported version of the validator is the latest copy - that is now R5. I don't take bug fixes for the older versions of the validator

Kevin Mayfield (Mar 26 2019 at 07:39):

Understand that and that won't validate stu3 so we should look at moving fixes to stu3.... or is their another way?

Grahame Grieve (Mar 26 2019 at 07:39):

it will validate stu3

Grahame Grieve (Mar 26 2019 at 07:39):

you just load all the R3 structure definitions into it, and tell it to validate your R3 content.

Grahame Grieve (Mar 26 2019 at 07:40):

(you do need to convert the R3 structure definitions and value sets etc to R5 using the R3/R5 converter as you load them)

Grahame Grieve (Mar 26 2019 at 07:41):

but you don't need to convert the resource you are validating - just validate the bytes directly

Kevin Mayfield (Mar 26 2019 at 07:41):

That's very welcome news

Grahame Grieve (Mar 26 2019 at 07:41):

going flying. back later

Morten Ernebjerg (Mar 26 2019 at 08:28):

Just to clarify, does one also need to explicitly transform STU3 structure defs/valsets/etc. before loading them when using the JAR validator from the command line? The current documentation says (when discussing loading IGs/profiles):

Packages must have the same underlying fhir version as that specified in the -version parameter

which sounds like one should use STU3 profiles when validating for STU3...?

Grahame Grieve (Mar 26 2019 at 21:10):

if you use the command line validator, then it does the conversion internally - if you say -version 3.0 then any resources loaded from the various packages (core + IGs) will be converted from R3 to R5

Grahame Grieve (Mar 26 2019 at 21:12):

what I said above about doing the conversion only applies if you are loading the validator java classes directly (or to be precise, if you are using org.hl7.fhir.r5.validation.InstanceValidator, not using org.hl7.fhir.r5.validation.ValidationEngine)

Morten Ernebjerg (Mar 27 2019 at 07:27):

OK, thanks for the clarification @Grahame Grieve !

Kevin Mayfield (Mar 27 2019 at 10:43):

Testing at the moment. I'm (temp) using r4 validator in HAPI but it seems to be working.
Need to see how it handles backport extensions - do they get converted?

Grahame Grieve (Mar 27 2019 at 11:48):

backport extensions?

Kevin Mayfield (Mar 27 2019 at 12:00):

backported

Grahame Grieve (Mar 27 2019 at 12:03):

no you have to define them

Kevin Mayfield (Mar 27 2019 at 12:03):

not the standard ones?

Grahame Grieve (Mar 27 2019 at 12:35):

if they're defined for STU3 then they'll be valid

Kevin Mayfield (Mar 27 2019 at 14:04):

I think this is an issue in HAPI 3.8.0-SNAPSHOT (their are others).
The Bundle CodeSystems appear to have the wrong url in
https://raw.githubusercontent.com/jamesagnew/hapi-fhir/master/hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/valueset/valuesets.xml

Kevin Mayfield (Mar 27 2019 at 14:04):

observation-category has url of <url value="http://terminology.hl7.org/CodeSystem/observation-category"></url>

Kevin Mayfield (Mar 27 2019 at 14:06):

and that matches the spec.

Kevin Mayfield (Mar 27 2019 at 14:06):

Ignore above.... I'll research a bit more. Appears to be a stu3 to r4 change

Kevin Mayfield (Mar 29 2019 at 16:03):

Should the converter also handle extensions that have changed e.g.

http://hl7.org/fhir/StructureDefinition/patient-birthPlace was in stu3 http://hl7.org/fhir/StructureDefinition/birthPlace

also

http://terminology.hl7.org/CodeSystem/v3-MaritalStatus was in stu3 http://hl7.org/fhir/v3/MaritalStatus

I may have missed off a conversion step.

Grahame Grieve (Mar 29 2019 at 19:10):

I'm not sure what you mean by changed - if you load the R3 definitions, then it should be looking for the R3 extension

Kevin Mayfield (Mar 30 2019 at 07:41):

That makes sense, will try that next.

This is the correct location for the converters https://github.com/jamesagnew/hapi-fhir/tree/master/hapi-fhir-converter
I'm using the stu3->r4 convertor at present , I've not seen support for r5 (and assumed that's a work in progress)

Kevin Mayfield (Mar 30 2019 at 09:23):

Using the stu3->r4 convertor returns
Caused by: org.hl7.fhir.exceptions.FHIRException: Unknown resource Procedure
When converting a Bundle with a Procedure.

Kevin Mayfield (Mar 30 2019 at 09:24):

at org.hl7.fhir.convertors.VersionConvertor_30_40.convertResource(VersionConvertor_30_40.java:21342) ~[hapi-fhir-converter-3.8.0-SNAPSHOT.jar:?]

Kevin Mayfield (Mar 30 2019 at 09:46):

Other than that, it's working. Just need to tweak the r4 DefaultProfileValidationSupport.class to load stu3 resources.
https://github.com/nhsconnect/careconnect-reference-implementation/blob/3.8/cc-core/src/main/java/uk/org/hl7/fhir/validation/r4/DefaultProfileValidationSupportStu3AsR4.java

Patrick Werner (Mar 30 2019 at 14:13):

@Kevin Mayfield
here is the current source of the validator and other FHIR core parts of hapi: https://github.com/hapifhir/org.hl7.fhir.core

Kevin Mayfield (Mar 31 2019 at 07:49):

Cheers. Are these outputting maven resources?

Grahame Grieve (Mar 31 2019 at 10:26):

the core code is all maven yes

Wan Chen (Apr 22 2019 at 17:49):

Hi folks, we have a DSTU2 Immunization that we would like to convert to R4. We are getting this error:
“org.hl7.fhir.exceptions.FHIRException: Unknown resource Immunization
at org.hl7.fhir.convertors.VersionConvertor_10_40.convertResource(VersionConvertor_10_40.java:12147)”
Looking at the HAPI converter code https://github.com/jamesagnew/hapi-fhir/blob/master/hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_40.java#L11978, the code does not support Immunizations.

Is there another FHIR Mapping Language Java implementation that does support Immunizations and the complete set of mappings? If not, should I write the code and create a pull request?

Grahame Grieve (Apr 22 2019 at 21:42):

there is nothing else. A pull request would be very welcome

Wan Chen (Apr 23 2019 at 14:30):

Thanks @Grahame Grieve!

Last updated: Apr 12 2022 at 19:14 UTC